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Continued development of ChEBI towards better usability for the systems biology and metabolic modelling community

持续开发 ChEBI，以提高系统生物学和代谢建模社区的可用性

基本信息

批准号：
BB/K019783/1
负责人：
Douglas Kell
金额：
$ 87.02万
依托单位：
University of Manchester
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2013
资助国家：
英国
起止时间：
2013 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FK019783%2F1
关键词：
Continued development ChEBI towards better

项目摘要

After a century of studying nature in greater and greater detail, generating the "parts list" of the molecular components within the cell, the biological sciences have undergone a paradigm shift in the last decade, moving towards putting together these individual molecular pieces to understand their interactions in a holistic context. It is these interactions which give rise to overall cellular processes, and their study has has been termed systems biology.Systems biology brings together a wide range of information about cells, genes and proteins, as well as the small molecules that act on and within these biological structures. In the service of its application areas, such as drug discovery and industrial biotechnology, it gives a holistic perspective aiming to track and eventually simulate the entire functioning of biological systems. In order to build up such holistic models from such a vast collection of diverse data, integration of individual units of information from many diverse databases needs to be performed. This integration of such a high volume of data can only feasibly be performed computationally. To facilitate smooth integration, individual molecular components within the cellular system require stable and unique identifiers. These identifiers are assigned to entities such as genes, proteins or small molecules by standardization bodies and database providers, and effectively allow the molecular parts list to be catalogued. In addition to this, human-relevant information such as names and chemical and biological structures, relationships and properties are also associated with the various entities in the databases, providing resources that are useable by both software tools and researchers themselves.The database Chemical Entities of Biological Interest (ChEBI) acts as a resource for such information and stable identifiers in the area of small molecules of biological interest. ChEBI provides for the bioscientific community semantic, biological and chemical information as well as stable identifiers for small chemical compounds relevant in biology, including the so-called metabolites. Metabolites are small molecules in organisms that are implicated in diverse processes including supplying the body with energy, serving as building blocks for tissue, and acting as a defence or as a signal within the organism or between organisms. For these purposes, ChEBI is widely used in the bioscience community, which sends formal requests for the assignment of identifiers for particular small molecule entities to the ChEBI team, who then perform the assignment, publish the information into the public domain and inform the requesting party that the request has been fulfilled.The aim of the current proposal is to further develop the ChEBI resource and create surrounding tools towards comprehensively addressing the chemical informatics (software and data) needs of the systems biology and metabolic modelling communities, so that they in turn can further their objective to create meaningful simulations and models that enable whole-systems research into pressing public health and energy challenges. In order to facilitate this use, we propose to:1. Develop a comprehensive software library for accessing ChEBI programmatically which will work across all major available operating systems;2. Extend the ChEBI database resource to enhance stability, increase community involvement, add additional biologically relevant relationships, and provide a new powerful visualisation for the biological context of molecular entities;3. Curate into ChEBI all known metabolites across important organisms in systems biology studies: human, mouse, E. coli and yeast.4. Create new training materials and delivery of training courses to the community.

经过一个世纪对自然界越来越详细的研究，产生了细胞内分子成分的“零件清单”，生物科学在过去十年中经历了一次范式转变，转向将这些单独的分子片段放在一起，以了解它们在整体背景下的相互作用。正是这些相互作用引起了整个细胞过程，它们的研究被称为系统生物学。系统生物学汇集了关于细胞，基因和蛋白质以及作用于这些生物结构和生物结构内的小分子的广泛信息。在其应用领域的服务，如药物发现和工业生物技术，它提供了一个全面的视角，旨在跟踪并最终模拟生物系统的整个功能。为了从如此大量的不同数据中建立这样的整体模型，需要对来自许多不同数据库的单个信息单元进行整合。如此大量的数据的这种整合只能通过计算来可行地执行。为了促进顺利整合，细胞系统内的单个分子组分需要稳定且独特的标识符。这些标识符由标准化机构和数据库提供商分配给基因、蛋白质或小分子等实体，并有效地允许对分子部件列表进行编目。除此之外，与人类相关的信息，如名称、化学和生物学结构、关系和性质，也与数据库中的各种实体相关联，提供了软件工具和研究人员自己都可以使用的资源。生物学感兴趣的化学实体数据库（ChEBI）是生物学感兴趣的小分子领域的此类信息和稳定标识符的资源。ChEBI为生物科学界提供语义，生物和化学信息以及与生物学相关的小化学化合物的稳定标识符，包括所谓的代谢物。代谢物是生物体中的小分子，参与各种过程，包括为身体提供能量，作为组织的构建块，以及作为生物体内或生物体之间的防御或信号。出于这些目的，ChEBI广泛用于生物科学界，其向ChEBI团队发送分配特定小分子实体标识符的正式请求，然后由ChEBI团队执行分配，将信息发布到公共领域，并通知请求方请求已得到满足。当前提案的目的是进一步开发ChEBI资源，并创建相关工具，全面解决系统生物学和代谢建模界的化学信息学（软件和数据）需求，使他们能够进一步实现其目标，即创建有意义的模拟和模型，使全系统研究能够应对紧迫的公共卫生和能源挑战。为了方便使用，我们建议：1。开发一个全面的软件库，用于以编程方式访问ChEBI，该软件库将在所有主要可用的操作系统上工作;2.扩展ChEBI数据库资源，以提高稳定性，增加社区参与，添加额外的生物相关关系，并为分子实体的生物背景提供新的强大的可视化;3.将系统生物学研究中重要生物体的所有已知代谢物纳入ChEBI：人、小鼠、大肠杆菌。大肠杆菌和酵母菌。创建新的培训材料，并向社区提供培训课程。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

21 世纪的标识符：如何设计、提供和重用持久标识符以最大限度地提高生命科学数据的效用和影响

DOI：
10.1101/117812
发表时间：
2017
期刊：
影响因子：
0
作者：
McMurry J
通讯作者：
McMurry J

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly.

DOI：
10.1016/j.tips.2015.07.006
发表时间：
2015-11
期刊：
Trends in pharmacological sciences
影响因子：
13.8
作者：
Mendes P;Oliver SG;Kell DB
通讯作者：
Kell DB

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

DOI：
10.1186/s12859-015-0486-3
发表时间：
2015-02-21
期刊：
BMC bioinformatics
影响因子：
3
作者：
Moreno P;Beisken S;Harsha B;Muthukrishnan V;Tudose I;Dekker A;Dornfeldt S;Taruttis F;Grosse I;Hastings J;Neumann S;Steinbeck C
通讯作者：
Steinbeck C

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.